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I tried uninstalling some applications, and files in these folders or the corresponding folders in ~/Library/Containers/ were sometimes deleted and sometimes not:

~/Library/Caches/ (deleted for most applications)

~/Library/Application Support/

Files in these folders weren't deleted for any of the applications I tested with:

~/Library/Preferences/

~/Library/Saved Application State/

/var/db/receipts/

~/Library/Logs/DiagnosticReports/

~/Library/Application Support/CrashReporter/

~/Library/Caches/com.plausiblelabs.crashreporter.data/

~/Library/Application Support/Growl/Tickets/

For example Kindle books or the database for notes in JustNotes were not deleted.

You can see what files are accessed by uninstalld with sudo opensnoop -n uninstalld and search for support files with mdfind $(osascript -e 'id of app "AppName"'). If you want to uninstall applications more completely, it's probably safe to just delete the whole sandbox containers in ~/Library/Containers/.

Maybe Apple records which one of the two contradictions is respected by developers of an app, then uninstalld refers to that record when evaluating whether it's acceptable to remove application support data. It's not acceptable to remove user data.
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Graham PerrinAug 2 '12 at 2:49

Thank you for this answer. This helps me understand the system better. So what gets removed is the decision of the developers? :-)
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eprilliosAug 2 '12 at 10:34

@GrahamPerrin Sorry, I forgot to post a comment after rolling back your edit. I think "user data" can mean both documents that would normally be opened by the user and something like SQLite files.
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ؘؘؘؘAug 2 '12 at 12:19

@Lri no problem, the content was easily replaced as a comment. As an example, I never liked Microsoft's use of ~/Documents for databases of user data (for Outlook etc.); ~/Library/Application Support seemed more appropriate. I still don't like to find databases – not human readable – amongst my readable documents. If Apple's guidance to developers is changing, I wonder about the motivation. Maybe WWDC 2012 videos, or other developer documentation, will hold clues. Meantime, my first guess is that future plans for iCloud play a part.
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Graham PerrinAug 2 '12 at 13:02